Details for: SCRT1

Gene ID: 83482

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: SCRT1

Ensembl ID: ENSG00000261678

Description: scratch family transcriptional repressor 1

Cell Significance Landscape

Associated with

  • Dna-binding transcription factor activity
    (GO:0003700)
  • Dna-binding transcription factor activity, rna polymerase ii-specific
    (GO:0000981)
  • Dna-binding transcription repressor activity, rna polymerase ii-specific
    (GO:0001227)
  • Metal ion binding
    (GO:0046872)
  • Negative regulation of transcription by rna polymerase ii
    (GO:0000122)
  • Nuclear body
    (GO:0016604)
  • Regulation of dna-templated transcription
    (GO:0006355)
  • Regulation of neuron migration
    (GO:2001222)
  • Rna polymerase ii cis-regulatory region sequence-specific dna binding
    (GO:0000978)
  • Rna polymerase ii transcription regulatory region sequence-specific dna binding
    (GO:0000977)
  • Sequence-specific dna binding
    (GO:0043565)
  • Sequence-specific double-stranded dna binding
    (GO:1990837)

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • retinal ganglion cell CL0000740
    CSI 5.21
    rCSI 11.5%
    PRS 94.67
  • rod bipolar cell CL0000751
    CSI 3.03
    rCSI 5.44%
    PRS 96.39
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 2.6
    rCSI 3.33%
    PRS 97.43
  • sst GABAergic cortical interneuron CL4023017
    CSI 2.55
    rCSI 3.29%
    PRS 95.48
  • cerebral cortex GABAergic interneuron CL0010011
    CSI 2.41
    rCSI 7.11%
    PRS 98.27
  • retinal bipolar neuron CL0000748
    CSI 2.4
    rCSI 4.49%
    PRS 95.46
  • retina horizontal cell CL0000745
    CSI 2.23
    rCSI 3.39%
    PRS 97.09
  • inhibitory interneuron CL0000498
    CSI 2.18
    rCSI 5.03%
    PRS 95.17
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 2.16
    rCSI 2.69%
    PRS 94.01
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 1.95
    rCSI 3.45%
    PRS 94.87

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

Comma-separated if multiple.
Comma-separated if multiple.
Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [SCRT1](/details-gene/83482) (scratch family transcriptional repressor 1) is a protein-coding gene located on chromosome 8q24.3. It encodes a zinc-finger transcription factor that belongs to the Snail superfamily. As its name implies, [SCRT1](/details-gene/83482) primarily functions as a transcriptional repressor, specifically inhibiting transcription mediated by RNA polymerase II. Expression data indicates a highly specialized role for [SCRT1](/details-gene/83482) within the central nervous system, where it is a significant marker for various neuronal subtypes, most notably in the retina and for inhibitory interneurons in the cerebral cortex. This is consistent with early research identifying it as a neural-specific transcriptional repressor ([Link](https://doi.org/10.1073/pnas.051014098)). ## Cellular Roles and Expression Landscape The expression profile of [SCRT1](/details-gene/83482) underscores its specialized function in the nervous system. **Overall**, the gene shows the highest significance in neuronal populations, particularly within the retina. It is a top marker for `[retinal ganglion cell](/details-cell/CL0000740)` (CSI: 5.21), `[rod bipolar cell](/details-cell/CL0000751)` (CSI: 3.03), `[retinal bipolar neuron](/details-cell/CL0000748)` (CSI: 2.40), and `[retina horizontal cell](/details-cell/CL0000745)` (CSI: 2.23), suggesting a fundamental role in establishing or maintaining the identity and function of these distinct retinal layers. Beyond the retina, [SCRT1](/details-gene/83482) is also a key marker for several classes of inhibitory neurons. It is highly significant in `[sst GABAergic cortical interneuron](/details-cell/CL4023017)` (CSI: 2.55), `[cerebral cortex GABAergic interneuron](/details-cell/CL0010011)` (CSI: 2.41), and `[pvalb GABAergic cortical interneuron](/details-cell/CL4023018)` (CSI: 2.16). Its strong association with developing neuronal precursors, such as `[neuroblast (sensu Vertebrata)](/details-cell/CL0000031)` (CSI: 2.60), further suggests a role during neurogenesis and neuronal differentiation. The collective expression pattern points to [SCRT1](/details-gene/83482) being a critical regulator of cell fate specification and functional maturation in specific neuronal lineages. ## Pathways and Molecular Function Functional annotation aligns closely with the observed expression pattern of [SCRT1](/details-gene/83482). Its primary molecular function is as a `[Dna-binding transcription repressor activity, rna polymerase ii-specific](/details-cell/GO:0001227)`, acting through `[Rna polymerase ii cis-regulatory region sequence-specific dna binding](/details-cell/GO:0000978)`. This activity is central to its role in biological processes such as `[Negative regulation of transcription by rna polymerase ii](/details-cell/GO:0000122)` and the broader `[Regulation of dna-templated transcription](/details-cell/GO:0006355)`. Crucially, [SCRT1](/details-gene/83482) is implicated in the `[Regulation of neuron migration](/details-cell/GO:2001222)`. This function is consistent with its high expression in developing neuroblasts and specific interneuron populations, which undergo extensive migration to reach their final positions in the cortex. As a transcription factor, [SCRT1](/details-gene/83482) localizes to the `[Nuclear body](/details-cell/GO:0016604)`, where it exerts its regulatory effects on target genes to orchestrate these complex developmental processes. ## Research Directions Given its specific expression pattern and function as a transcriptional repressor, [SCRT1](/details-gene/83482) presents several avenues for future investigation into nervous system development and disease. **Proposed Hypotheses:** 1. Given its high and specific expression across multiple, distinct retinal neuron types, [SCRT1](/details-gene/83482) may function as a master regulator that controls a core transcriptional program essential for the terminal differentiation and long-term survival of post-mitotic retinal neurons. 2. Based on its involvement in `[Regulation of neuron migration](/details-cell/GO:2001222)` and its high significance in GABAergic interneuron subtypes, [SCRT1](/details-gene/83482) likely directs the tangential migration and proper laminar integration of cortical interneurons during embryonic brain development by repressing genes that promote alternative cell fates or inhibit migration. **Experimental Approach:** To test the hypothesis that [SCRT1](/details-gene/83482) is essential for retinal neuron differentiation (Hypothesis 1), a powerful approach would be to use human induced pluripotent stem cell (iPSC)-derived retinal organoids. A [SCRT1](/details-gene/83482) knockout iPSC line could be generated using CRISPR-Cas9 gene editing. The development of these knockout organoids would be compared to isogenic wild-type controls over time. A combination of single-cell RNA sequencing (scRNA-seq) and immunohistochemistry for mature retinal markers would be used to determine if the loss of [SCRT1](/details-gene/83482) leads to a failure in generating specific cell types (e.g., retinal ganglion cells, bipolar cells) or a block in their maturation. **Therapeutic Potential:** As an intracellular transcription factor, [SCRT1](/details-gene/83482) is a challenging target for conventional small molecule or antibody-based therapies. However, its high neuronal specificity makes it an interesting candidate for gene therapy approaches. In neurodevelopmental disorders or retinal degenerative diseases linked to [SCRT1](/details-gene/83482) dysregulation, restoring its normal expression level and function via viral vectors could be a viable long-term strategy. The therapeutic goal would likely be the precise modulation of its activity rather than simple inhibition, depending on whether a loss-of-function or gain-of-function mechanism underlies the pathology.

Genular Protein ID: 48538548

Symbol: SCRT1_HUMAN

Name: Transcriptional repressor scratch 1

UniProtKB Accession Codes:

Q9BWW7 A8MX66 Q96C52

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CTD 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 3 Ensembl 2 GO 12 Gene3D 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 3 KEGG 1 MANE-Select 1 MIM 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PROSITE 2 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 2 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 RNAct 1 RefSeq 1 SMART 1 SMR 1 STRING 1 SUPFAM 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 11274425

Title: Mammalian scratch: a neural-specific snail family transcriptional repressor.

PubMed ID: 11274425

DOI: 10.1073/pnas.051014098

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

Sequence Information:

  • Length: 348
  • Mass: 35554
  • Checksum: D3BB51709C7795DA
  • Sequence:
    • MPRSFLVKKV KLDAFSSADL ESAYGRARSD LGAPLHDKGY LSDYVGPSSV YDGDAEAALL 
KGPSPEPMYA AAVRGELGPA AAGSAPPPTP RPELATAAGG YINGDAAVSE GYAADAFFIT 
DGRSRRKASN AGAAAAPSTA SAAAPDGDAG GGGGAGGRSL GSGPGGRGGT RAGAGTEARA 
GPGAAGAGGR HACGECGKTY ATSSNLSRHK QTHRSLDSQL ARRCPTCGKV YVSMPAMAMH 
LLTHDLRHKC GVCGKAFSRP WLLQGHMRSH TGEKPFGCAH CGKAFADRSN LRAHMQTHSA 
FKHFQCKRCK KSFALKSYLN KHYESACFKG GAGGPAAPAP PQLSPVQA